AIMC Topic: Biological Ontologies
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Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network.
Journal of biomedical informatics
Jun 3, 2015
Biomedical ontologies are a critical component in biomedical research and practice. As an ontology evolves, its structure and content change in response to additions, deletions and updates. When editing a biomedical ontology, small local updates may ...
Interactive Cohort Identification of Sleep Disorder Patients Using Natural Language Processing and i2b2.
Applied clinical informatics
May 27, 2015
UNLABELLED: Nationwide Children's Hospital established an i2b2 (Informatics for Integrating Biology & the Bedside) application for sleep disorder cohort identification. Discrete data were gleaned from semistructured sleep study reports. The system sh...
Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies.
Systematic biology
May 26, 2015
The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in noncompu...
A formal concept analysis and semantic query expansion cooperation to refine health outcomes of interest.
BMC medical informatics and decision making
May 20, 2015
BACKGROUND: Electronic Health Records (EHRs) are frequently used by clinicians and researchers to search for, extract, and analyze groups of patients by defining Health Outcome of Interests (HOI). The definition of an HOI is generally considered a co...
Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy.
Database : the journal of biological databases and curation
May 13, 2015
The diverse phenotypes of living organisms have been described for centuries, and though they may be digitized, they are not readily available in a computable form. Using over 100 morphological studies, the Phenoscape project has demonstrated that by...
The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.
Database : the journal of biological databases and curation
May 9, 2015
Biocuration has become a cornerstone for analyses in biology, and to meet needs, the amount of annotations has considerably grown in recent years. However, the reliability of these annotations varies; it has thus become necessary to be able to assess...
Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.
PloS one
Apr 20, 2015
The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation o...
Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.
Database : the journal of biological databases and curation
Apr 4, 2015
Bio-ontologies provide terminologies for the scientific community to describe biomedical entities in a standardized manner. There are multiple initiatives that are developing biomedical terminologies for the purpose of providing better annotation, da...
Integrating ontologies of rare diseases and radiological diagnosis.
Journal of the American Medical Informatics Association : JAMIA
Mar 31, 2015
PURPOSE: The author sought to integrate an ontology of rare diseases with a large ontological model of radiological diagnosis.
MorphoCol: An ontology-based knowledgebase for the characterisation of clinically significant bacterial colony morphologies.
Journal of biomedical informatics
Mar 25, 2015
BACKGROUND: One of the major concerns of the biomedical community is the increasing prevalence of antimicrobial resistant microorganisms. Recent findings show that the diversification of colony morphology may be indicative of the expression of virule...
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